Module 1: V5 - V12

Question 1

What are the many functions of protein in the body?

Answer 1

catalysis (enolase, DNA polymerase)
transport (hemoglobin, GLUT1)
structure (collagen, keratin)
motion (myosin, actin)
signaling (insulin receptor
glucagon receptor)

Question 2

What are the properties of amino acids?

Answer 2

capacity to polymerize, useful acid-base properties, varied physical properties, varied chemical functionality

Question 3

Do most naturally occurring proteins consist of D or L-amino acids?

Answer 3

L-amino acids

Question 4

What does D and L mean?

Answer 4

based on rotation of plane of polarised light viewed towards the light source
D - right or clockwise rotation (do not all)
L - left or anti-clockwise rotation (do not all)

Question 5

How do you determine whether an amino acid is D or L?

Answer 5

look down the Ha-Ca bond with Ha at the front

an L-amino acid will read CORN in a clockwise direction (CO = carboxylate group, R = R group, N = amine group)

Question 6

What is pKa?

Answer 6

pKa is pH when there is a 1:1 ratio of products and reactants

Question 7

Which amino acids have acidic side chains? Are they ionised at physiological pH (7.4)?

Answer 7

aspartic acid and glutamic acid

yes, because they are neutral at a pH below 4.4 and negatively charged at a pH above 4.4

Question 8

Which residues would you expect to find in a calcium binding site?

Answer 8

aspartic acid and glutamic acid because they often act as chelators of metal ions

Question 9

Which amino acids have basic side chains and what are their characteristics?

Answer 9

lysine, arginine and histidine
lysine and arginine have long aliphatic side chains of methylene groups capped respectively with amino and guanidino groups

Question 10

Is lysine ionised at physiological pH (7.4)?

Answer 10

yes, because lysine is neutral above a pH of 10 and positively charged below a pH of 10 (potent nucleophile)

Question 11

Is arginine ionised at physiological pH (7.4)?

Answer 11

yes, because arginine is neutral above a pH of 12 and positively charged below a pH of 12

Question 12

What are the characteristics of a guanidino group?

Answer 12

planar and stabilised by resonance

charge is delocalised over whole group (partial double bonds)

Question 13

Why is histidine often found in the active site of enzymes?

Answer 13

possesses a 5-membered imidazole ring which allows the amino acid to be chemically ambidextrous
this is because the ring has two nitrogen atoms which are both H-bond donors/acceptors and can be either electrophiles or nucleophiles
therefore, histidine is often found in the active sites of enzymes as they allow for all sorts of reactions to proceed

Question 14

Is histidine ionised at physiological pH (7.4)?

Answer 14

both states are well populated at pH 7.4 as the pKa of histidine is 7

Question 15

Which amino acids have uncharged polar side chains (amides) and what are their characteristics?

Answer 15

asparagine and glutamine possess one/two methylenes capped by amide groups
they are not very chemically reactive
they deamidate to aspartic acid and glutamic acid
group is planar like peptide bond

Question 16

Which amino acids have uncharged polar side chains (hydroxyls) and what are their characteristics?

Answer 16

serine and threonine
not very chemically reactive
threonine has an extra chiral centre

Question 17

Which amino acids are aromatic and what are their characteristics?

Answer 17

phenylalanine is nonpolar and unreactive
tyrosine hydroxyl group pKa is around 10
tryptophan indole ring has conjugated double bonds (largest side chain)

Question 18

Which peptides absorb UV light and why?

Answer 18

peptides which are consisted of amino acids with aromatic side chains
this is because the extent and geometry of conjugated double bond systems cause spectral differences which is useful for the detection of proteins in solution

Question 19

How do aromatic side chains allow us to determine protein structure?

Answer 19

the spectral properties of these side chains are sensitive to their immediate environment meaning that we can determine if certain amino acids are buried or exposed

Question 20

Which amino acids are non-polar and what are their characteristics?

Answer 20

alanine and valine have nonpolar side chains
leucine is a longer version of valine and isoleucine is “beta-branched” + has a chiral centre
proline is a cyclic five-membered ring and glycine has no side chain

Question 21

Which amino acids contain sulfur and what are their characteristics?

Answer 21

cysteine and methionine
cysteine is partially deprotonated at pH 7 and is very reactive when deprotonated
methionine is nonpolar and not particularly reactive

Question 22

Is cysteine ionised at physiological pH (7.4)?

Answer 22

yes, will be neutral at a pH below 8.5 and negatively charged (deprotonated) at a pH above 8.5

Question 23

Which amino acids form disulfide bonds? How do oxidising and reducing conditions affect disulfide bonding?

Answer 23

cysteine is able to form disulfide bonds under oxidising conditions
cysteine is not able to form disulfide bonds under reducing conditions

Question 24

Would you expect to find the Gln side chain acting as a hydrogen bond donor or acceptor?

Answer 24

glutamine can act as a hydrogen bond donor and acceptor (uncharged polar amino acids are hydrogen bond donors and acceptors)

Question 25

Where do oxidising conditions exist? Outside or inside the cell?

Answer 25

outside the cell

Question 26

Where do reducing conditions exist? Outside or inside the cell?

Answer 26

inside the cell

Question 27

Why is protein concentration often measured using A(absorbance at 280 nm)?

Answer 27

this is because absorbance is proportional to the protein concentration in solution